]> Biopharma Reference Ontology Attributes This ontology serves as a staging area for candidate common attribute constructs assembled within BMIC. The content includes attributes that may apply across different kinds of bearers, including materials and equipment. These constructs support consistent attribute modeling across BMIC ontologies and provide candidate content for future inclusion in an IOF mid-level ontology, with the Materials Science and Engineering group expected to be the main target for many of these constructs. Adlane Rebai, Millipore Sigma Ana Nikolov, OAGi Boonserm Kulvatunyou, NIST Cameron Gibbs, CrownPoint Technologies, LLC Gabriela Henning, NIST Jan Kemper, AstraZeneca Marie-Aude Coutouly, Millipore Sigma Melissa Weller, CrownPoint Technologies, LLC Milos Drobnjakovic, OAGi Stephen J. Granite, CrownPoint Technologies, LLC Stephen Kahmann, CrownPoint Technologies, LLC NIIMBL BD-1 Ontology Group http://opensource.org/licenses/MIT BMIC Biopharma Reference Ontology Attributes

adhesion https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ protein formulation residue adhering to a vial wall; cells adhering to a microcarrier surface; a label adhesive adhering to a syringe barrel;

Adhesion(x) → RelationalQuality(x) ∧ ∃m1∃m2 (MaterialEntity(m1) ∧ MaterialEntity(m2) ∧ m1 ≠ m2 ∧ qualityOf(x, m1) ∧ qualityOf(x, m2))

true

relational quality of two material entities that is the extent to which those entities are held together through interactions at their contacting surfaces

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'adhesion' then x is a 'relational quality' that is the 'quality of' at least two distinct 'material entities'

age https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Age of a raw material lot assessed relative to its manufacture date; Age of a prepared buffer assessed relative to its preparation time; Age of a cell culture assessed relative to thaw or inoculation according to the applicable convention; Age of a drug substance batch assessed relative to production or fill date; Age of a single-use assembly assessed relative to manufacture or sterilization date

http://purl.obolibrary.org/obo/PATO_0000011

Age is the quality itself, while an age value, such as “14 days” or “6 months,” is an information content entity or value expression that describes that quality. The starting point for determining age depends on the kind of bearer and the relevant domain convention, for example manufacture date, thaw date, birth, creation, preparation, or assembly.

Age(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality of a material entity determined by the elapsed time since a specified reference event associated with that material entity

This term is expected to remain primitive

if x is an 'age' then x is a 'quality' that is the 'quality of' some 'material entity'

aggregate state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the solid aggregate state of sodium chloride crystals; the liquid aggregate state of a buffer solution; the gaseous aggregate state of cleanroom air; the plasma aggregate state of an ionized gas; the solid aggregate state of powdered cell culture medium

http://purl.allotrope.org/ontologies/quality#AFQ_0000111

AggregateState(x) → Quality(x) ∧ ∃m(MaterialEntity(m) ∧ qualityOf(x,m))

true

quality of a material entity that is the physical state in which that material entity exists, such as solid, liquid, gaseous, or plasma

This term is expected to remain primitive

if x is an 'aggregate state' then x is a 'quality' that is the 'quality of' some 'material entity'

state of matter

amorphous structure https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the amorphous structure of a lyophilized protein formulation cake; the amorphous structure of spray-dried lactose; the amorphous structure of an amorphous solid dispersion containing a poorly soluble drug substance; the amorphous structure of glass;

https://en.wikipedia.org/wiki/Amorphous_solid

AmorphousStructure(x) → PhysicalStructure(x) ∧ ∃m∃s (MaterialEntity(m) ∧ qualityOf(x, m) ∧ SolidAggregateState(s) ∧ hasQuality(m, s))

true

physical structure that inheres in a solid material entity by virtue of the material entity lacking the long-range order characteristic of a crystalline structure

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'amorphous structure' then x is a 'physical structure' that is the 'quality of' some 'material entity' that 'has quality' some 'solid aggregate state'

area https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Surface area of a chromatography resin bead; Cross-sectional area of a tubing lumen; Membrane area of a filtration device; Contact area of a single-use bag surface exposed to process material; Surface area of a powder particle;

http://purl.obolibrary.org/obo/PATO_0001323

Area(x) → PhysicalSize(x)

true

physical size that is the two-dimensional spatial extent of a bearer over a particular surface

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'area' then x is a 'physical size'

color https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ yellow color of phenol red in acidified cell culture medium; reddish-orange color of phenol red in medium near physiological pH; pink or purple color of phenol red in alkaline medium; Yellow discoloration of a formulation sample during stability testing; Brown color of a degraded raw material solution; Color of a cell culture medium lot assessed during visual inspection;

http://purl.obolibrary.org/obo/PATO_0000014

Color(x) → OpticalQuality(x)

true

optical quality characterized by hue, saturation, and intensity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'color' then x is an 'optical quality'

compositional homogeneity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Compositional homogeneity of a prepared culture medium lot, where its dissolved constituents are uniformly distributed throughout the lot; Compositional homogeneity of a buffer preparation, where the buffer components and salts are uniformly distributed throughout the prepared solution; Compositional homogeneity of a powdered cell culture medium blend, where the intended powder constituents are uniformly distributed throughout the blend;

CompositionalHomogeneity(x) → Homogeneity(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m) ∧ ∀y (hasMagnitudeBasisInBearerPart(x, y) → (MaterialEntity(y) ∧ isMadeOfAtSomeTime(m, y))))

true

homogeneity inhering in a material entity by virtue of the extent to which one or more constituents of that material entity are uniformly distributed throughout that material entity

There are insufficient constructs to create a set of necessary and sufficient conditions.

if x is a 'compositional homogeneity', then x is a 'homogeneity' that is the 'quality of' some 'material entity' m, and every entity y that x 'has magnitude basis in bearer part' is a 'material entity' that m 'is made of at some time'

count https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the viable cell count of a cell population; the particle count of a liquid drug product sample; the bead count of a microcarrier population; the colony count of a microbial colony population growing on an agar plate; the unit count of a manufactured lot; the vial count in a packaging batch; the pore count per square micrometer of a filter membrane

Count(x) → Quality(x) ∧ ∃m(MaterialEntity(m) ∧ qualityOf(x,m))

true

quality of a material entity that is the number of discrete sites or material entities of a particular kind that are present as parts of that material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'count' then x is a 'quality' that is the 'quality of' some 'material entity'

crystalline structure https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the crystalline structure of sodium chloride crystals; the crystalline structure of a crystalline drug substance lot; the crystalline structure of mannitol in a lyophilized formulation; the crystalline structure of lactose monohydrate powder;

https://en.wikipedia.org/wiki/Crystal

CrystallineStructure(x) → PhysicalStructure(x) ∧ ∃m∃s (MaterialEntity(m) ∧ qualityOf(x, m) ∧ SolidAggregateState(s) ∧ hasQuality(m, s))

true

physical structure that inheres in a solid material entity by virtue of the material entity having material parts arranged in a highly ordered, long-range periodic lattice

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'crystalline structure' then x is a 'physical structure' that is the 'quality of' some 'material entity' that 'has quality' some 'solid aggregate state'

density https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the number density of cells in a culture fluid; the number density of particles in cleanroom air; the mass density of a buffer solution; the radiant energy density in the interior of an irradiation chamber

Density(x) → RelationalQuality(x)

true

relational quality that is the magnitude of a particular quality per unit size of the bearer

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'density' then x is a 'relational quality'

diameter https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Diameter of a chromatography resin bead; Diameter of a spherical protein aggregate particle; Diameter of a tubing lumen in a single-use assembly; Diameter of a filter pore; Diameter of a bioreactor vessel; Diameter of a circular chromatography column bed.

http://purl.obolibrary.org/obo/PATO_0001334

Diameter(x) → Length(x)

true

length that is the straight-line spatial extent through the center of a circular or spherical bearer, measured between two opposite boundary points

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'diameter' then x is a 'length'

electric charge https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the electric charge of a sodium ion; the surface electric charge of a chromatography resin particle;

https://www.britannica.com/science/electric-charge and https://openstax.org/books/physics/pages/18-1-electrical-charges-conservation-of-charge-and-transfer-of-charge

ElectricCharge(x) → ElectricalQuality(x)

true

electrical quality of a material entity by virtue of which that material entity exerts or experiences electric force in an electric field

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'electric charge' then x is an 'electrical quality'

electrical conductivity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Electrical conductivity of a chromatography buffer measured before column equilibration; Electrical conductivity of purified water used for buffer preparation; Electrical conductivity of a cell culture medium lot during release testing;

http://purl.obolibrary.org/obo/PATO_0001585

ElectricalConductivity(x) → ElectricalQuality(x)

true

electrical quality that is the extent to which the material entity conducts electric charge in response to an electric field

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'electrical conductivity' then x is an 'electrical quality'

electrical quality https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the electric charge of a particle; the surface charge of a chromatography resin particle; the zeta potential of a colloidal suspension; the electric potential of an electrode; the relative permittivity of a dielectric material

ElectricalQuality(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality that inheres in a material entity by virtue of how that material entity interacts with electric charge or electric fields

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'electrical quality' then x is a 'quality' that is the 'quality of' some 'material entity'

fluid aggregate state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ liquid aggregate state of a buffer solution; the liquid aggregate state of a cell culture medium solution; the gaseous aggregate state of cleanroom air; the gaseous aggregate state of oxygen in a gas supply line; the plasma aggregate state of an ionized gas

FluidAggregateState(x) → AggregateState(x)

true

aggregate state of a material entity in which the material entity lacks a fixed shape and can undergo continuous deformation under shear, including liquid, gaseous, and plasma aggregate states

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'fluid aggregate state' then x is an 'aggregate state'

fraction https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the mass fraction of glucose in a powdered medium; the molar fraction of oxygen in a gas mixture; the volume fraction of ethanol in an aqueous solution; the solids fraction of a slurry; the volume fraction of gas in a foam; the mass fraction of water molecules in a lyophilized drug product cake

http://purl.allotrope.org/ontologies/quality#AFQ_0000172

Fraction(x) → Ratio(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

ratio of a material entity that is determined by the magnitude of a quality of a specified part of that material entity relative to the magnitude of a quality of the same kind of that material entity as a whole

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'fraction' then x is a 'ratio' that is the 'quality of' some 'material entity' y

gaseous aggregate state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the gaseous aggregate state of cleanroom air; the gaseous aggregate state of oxygen in a gas supply line; the gaseous aggregate state of carbon dioxide in a bioreactor headspace;

http://purl.allotrope.org/ontologies/quality#AFQ_0000114

GaseousAggregateState(x) → FluidAggregateState(x)

true

fluid aggregate state of a material entity in which the material entity has no fixed shape or fixed volume and tends to expand to fill the available volume of its container

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'gaseous aggregate state' then x is a 'fluid aggregate state'

granule form https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the granule form of granulated cell culture medium; the granule form of an excipient after wet granulation; the granule form of a dried buffer blend prepared to reduce dusting;

https://www.sigmaaldrich.com/RS/en/technical-documents/technical-article/microbiological-testing/microbial-culture-media-preparation/comparison-of-granulated-and-powdered-dehydrated-culture-media and https://www.edqm.eu/documents/52006/389906/standard_terms_internal_vocabularies_for_pharmaceutical_dose_forms.pdf/dd395dc1-4d44-9c2e-ce7f-0d788d57b328?t=1651562025434&

GranuleForm(x) → ParticulateForm(x)

true

particulate form that inheres in a material entity by virtue of the material entity being physically organized as discrete aggregate units composed of smaller bound solid particles

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'granule form' then x is a 'particulate form'

homogeneity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Homogeneity of glucose concentration throughout a prepared culture medium lot; Homogeneity of pH throughout a reconstituted buffer preparation; Homogeneity of trace element distribution throughout a powdered cell culture medium blend; Homogeneity of particle size distribution in a dry powder mixture; Homogeneity of osmolality across sublots of a prepared medium batch; Homogeneity of optical density in a well-mixed cell suspension

https://goldbook.iupac.org/terms/view/H02845

Homogeneity is always relative to what is being evaluated, such as a particular analyte, particle size fraction, moisture content, pH, osmolality, or optical density. When homogeneity concerns a quality, what is evaluated in practice is the uniformity of the values or observable manifestations of that quality across the material. The same quantity of material may be homogeneous with respect to one constituent or quality and heterogeneous with respect to another, because different constituents or qualities can vary differently across the material. For example, a powder blend may be homogeneous in total mass fraction of a salt but heterogeneous in trace element distribution; a reconstituted medium may be homogeneous in bulk pH but heterogeneous in dissolved gas concentration immediately after mixing.

Homogeneity(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality of a material entity that is the extent to which a particular constituent of that material entity, or a particular quality of that material entity, is uniformly distributed throughout that material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'homogeneity' then x is a 'quality' that is 'quality of' some 'material entity'

length https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Length of a tubing segment in a single-use assembly; Length of a chromatography column bed; Length of a fiber or filament in a raw material sample; Length of a needle used in a filling operation; Length of a particle measured along its longest dimension; Length of a bioreactor probe inserted into a vessel.

http://purl.obolibrary.org/obo/PATO_0000122

Length(x) → PhysicalSize(x)

true

physical size that is the one-dimensional spatial extent of a bearer between two boundary points along a particular direction

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'length' then x is a 'physical size'

liquid aggregate state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the liquid aggregate state of a buffer solution; the liquid aggregate state of a cell culture medium solution; the liquid aggregate state of purified water;

http://purl.allotrope.org/ontologies/quality#AFQ_0000113

LiquidAggregateState(x) → FluidAggregateState(x)

true

fluid aggregate state of a material entity in which the material entity has no fixed shape, conforms to the shape of its container, and has an approximately fixed volume

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'liquid aggregate state' then x is a 'fluid aggregate state'

mass https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Mass of a raw material lot recorded during incoming material receipt; Mass of sodium chloride weighed during buffer preparation; Mass of powdered cell culture medium dispensed for media preparation; Mass of a filled drug product vial measured during fill-weight verification;

http://purl.obolibrary.org/obo/PATO_0000125

Mass(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality of a material entity determined by the amount of matter in that material entity

This term is expected to remain primitive.

if x is a 'mass' then x is a 'quality' that is the 'quality of' some 'material entity'

mass density https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ mass density of purified water; the mass density of a buffer solution; the mass density of a cell culture medium; the mass density of a protein formulation;

http://purl.obolibrary.org/obo/PATO_0001019

MassDensity(x) → Density(x)

true

density of a material entity that is the mass of that material entity per unit size of that material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'mass density' then x is a 'density'

mass fraction https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the mass fraction of glucose in a powdered medium; the mass fraction of sodium chloride in a buffer formulation; the mass fraction of water molecules in a lyophilized drug product cake;

http://purl.allotrope.org/ontologies/quality#AFQ_0000173

MassFraction(x) → Fraction(x) ∧ ∃m(MaterialEntity(m) ∧ qualityOf(x,m) ∧ ∀p(hasMagnitudeBasisInBearerPart(x,p) → (MaterialEntity(p) ∧ properContinuantPartOfAtSomeTime(p,m))))

true

fraction of a material entity that is determined by the mass of a specified part of that material entity relative to the total mass of the material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'mass fraction' then x is a 'fraction' that is the 'quality of' some 'material entity' m, and if x 'has magnitude basis in bearer part' some p, then p is a 'material entity' that is a 'proper continuant part of at some time' that same material entity m

material form https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the powder form of a dry cell culture medium; the granular form of a granulated dry cell culture medium; the cake form of a lyophilized drug product; the caked form of a moisture-exposed powder blend; the compacted form of a powder blend; the pelletized form of a processed material; the bead form of a chromatography resin;

MaterialForm(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality that inheres in a material entity by virtue of how the material entity or its material parts are physically organized at a macroscopic scale

This term is expected to be formalized further in IOF Core or IOF MSE WG

if x is a 'material form' then x is a 'quality' that is the 'quality of' some 'material entity'

morphological quality https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Particle size of particles in a powdered raw material; Particle shape of particles in a dry media powder; Granule morphology of a granulated culture medium; Cell morphology of cells observed during cultivation; Aggregate morphology of protein particles in a formulation; Crystal morphology of a crystalline excipient or salt; Physical structure of granules in a granulated culture medium; Physical shape of crystals in a crystalline raw material.

http://purl.obolibrary.org/obo/PATO_0000051

MorphologicalQuality(x) → Quality(x)

true

quality inhering in the bearer by virtue of the bearer's size or shape or structure

This term is expected to remain primitive.

if x is a 'morphological quality' then x is a 'quality'

net electric charge https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the net electric charge of a protein molecule at pH 5.5;

https://www.britannica.com/science/electric-charge and https://openstax.org/books/physics/pages/18-1-electrical-charges-conservation-of-charge-and-transfer-of-charge

net electric charge is equal to the algebraic sum of all positive and negative electric charges borne by that entity

NetElectricCharge(x) → ElectricCharge(x)

true

electric charge that is the overall electric charge of a material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'net electric charge' then x is an 'electric charge'

number density https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the number density of cells in a culture fluid; the number density of particles in cleanroom air; the number density of viable cells in a cell suspension

http://purl.allotrope.org/ontologies/quality#AFQ_0000180

NumberDensity(x) → Density(x)

true

density that is the number of countable entities per unit size

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'number density' then x is a 'density'

number fraction https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the viable cell fraction of a cell population; the nonviable cell fraction of a cell population; the particle fraction of subvisible particles above a specified size threshold in a particle population; the fraction of beads with attached cells in a microcarrier population; the rejected unit fraction in a manufactured unit lot

http://purl.allotrope.org/ontologies/quality#AFQ_0000291

NumberFraction(x) → Fraction(x)

true

fraction of a material entity that is determined by the count of specified parts of that material entity relative to the total count of relevant parts of that material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'number fraction' then x is a 'fraction'

optical quality https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Color of a cell culture medium lot; Clarity of a buffer preparation; Turbidity of a process intermediate; Opacity of a suspension; Absorbance of a protein solution at 280 nm; Fluorescence of a labeled assay reagent; Light scattering of protein aggregate particles in a formulation sample; Visual appearance of a drug product solution during inspection.

http://purl.obolibrary.org/obo/PATO_0001300

OpticalQuality(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality that inheres in a material entity by virtue of how that material entity interacts with light

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is an 'optical quality' then x is a 'quality' that is the 'quality of' some 'material entity'

particle size distribution https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Particle size distribution of a powdered cell culture media lot reported as D10, D50, and D90 values from laser diffraction; Particle size distribution of a granulated media formulation reported as the percentage of particles within predefined size intervals; Particle size distribution of an excipient powder reported as retained mass fraction on a series of sieves; Particle size distribution of an excipient powder used in formulation, assessed to support flowability, mixing performance, and dose uniformity;

https://www.sciencedirect.com/topics/chemistry/particle-size-distribution

Particle size distribution describes a population-level morphological quality, not the size of a single particle. It may be represented using size-frequency or cumulative distribution data, such as the relative fraction of particles within defined size intervals or percentile-based descriptors such as D10, D50, and D90. Summary statistics such as mean particle size may be reported together with particle size distribution data, but a mean value alone does not fully characterize the distribution.

ParticleSizeDistribution(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m) ∧ ∃f (ParticulateForm(f) ∧ hasQuality(m, f)))

true

quality of a particle population that is the distribution of physical sizes of the particles in that population

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'particle size distribution' then x is a 'quality' that is the 'quality of' some 'material entity' that 'has quality' some 'particulate form'

particulate form https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the powder form of powdered cell culture medium; the granule form of granulated medium; the bead form of chromatography resin; the pelletized form of a pelletized raw material; the particulate form of spray-dried excipient particles;

https://www.cif.iastate.edu/files/inline-files/Particle%20Characterization%20Guide.pdf and https://www.iso.org/obp/ui/en/#iso:std:iso:26824:ed-2:v1:en and Materials Selection in Mechanical Design Ashby

Particulate form inheres in a material entity that is physically organized as discrete solid particles or particle aggregates, such as a powder, granule material, bead material, or pellet material. A liquid mixture that contains suspended particles, such as a slurry or suspension, should not be classified as having particulate form merely because it contains particles. In such cases, the particulate form may inhere in the suspended solid material or particle population, while the whole liquid mixture is classified by its mixture type.

ParticulateForm(x) → MaterialForm(x) ∧ ∃m∃s (MaterialEntity(m) ∧ qualityOf(x, m) ∧ SolidAggregateState(s) ∧ hasQuality(m, s))

true

material form that inheres in a material entity by virtue of being physically organized at a macroscopic scale as a collection of discrete solid particles or particle aggregates

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'particulate form' then x is a 'material form' that is the 'quality of' some 'material entity' that 'has quality' some 'solid aggregate state'

particulate load https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Particulate load of a drug product sample measured as the number of subvisible particles per mL; Particulate load of a buffer preparation assessed before filtration; Particulate load of a process intermediate after a hold step; Particulate load of a cell culture medium lot assessed during release testing; Particulate load of a formulation sample assessed by visual inspection for visible particles; Particulate load of purified water monitored as part of water-system quality control.

ParticulateLoad(x) → Quality(x) ∧ ∃m(MaterialEntity(m) ∧ qualityOf(x,m) ∧ ∀p(hasMagnitudeBasisInBearerPart(x,p) → (MaterialEntity(p) ∧ continuantPartOfAtSomeTime(p,m) ∧ ∃f(ParticulateForm(f) ∧ hasQuality(p,f)))))

true

quality of a material entity that is the extent to which particulate matter is present in the material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'particulate load' then x is a 'quality' that is the 'quality of' some 'material entity' m, and if x 'has magnitude basis in bearer part' some p, then p is a 'material entity' that is a 'continuant part of at some time' m and 'has quality' some 'particulate form'

photostability https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Photostability of a protein formulation exposed to visible or ultraviolet light; Photostability of a cell culture medium lot during storage in a translucent container; Photostability of a buffer or reagent exposed to laboratory lighting; Photostability of a light-sensitive excipient or vitamin-containing formulation.

https://www.ema.europa.eu/en/documents/scientific-guideline/ich-q-1-b-photostability-testing-new-active-substances-and-medicinal-products-step-5_en.pdf and https://www.collinsdictionary.com/us/dictionary/english/photostability#:~:text=the%20ability%20of%20a%20material,due%20to%20exposure%20to%20light

Photostability(x) → Stability(x)

true

stability that is the capability of a material entity to resist change in one or more of its attributes during light exposure

There are insufficient constructs to create a set of necessary and sufficient conditions.

if x is 'photostability' then x is a 'stability'

physical shape https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Spherical shape of chromatography resin beads; Elongated shape of fiber-like particles in a raw material sample; Irregular shape of powder particles in a dry cell culture media blend; Rounded granule shape in a granulated culture medium; Needle-like crystal shape in a crystalline excipient or salt; Spherical or irregular shape of protein aggregate particles in a formulation sample;

http://purl.obolibrary.org/obo/PATO_0000052

Examples of geometric features include points, edges, surfaces and holes

PhysicalShape(x) → MorphologicalQuality(x)

true

morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its geometric features

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'physical shape' then x is a 'morphological quality'

physical size https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Surface area of a chromatography resin bead; Cross-sectional area of a tubing lumen; Length of a tubing segment in a single-use assembly; Length of a chromatography column bed; Volume of a process intermediate collected after filtration; Internal volume of a single-use bag;

http://purl.obolibrary.org/obo/PATO_0000117

PhysicalSize(x) → MorphologicalQuality(x)

true

morphological quality that is the spatial extent of the bearer in one or more spatial dimensions

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'physical size' then x is a 'morphological quality'

physical structure https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Physical structure of a granulated culture medium by virtue of the arrangement of powder particles within granules; Physical structure of a crystalline excipient by virtue of its crystal lattice organization; Physical structure of a chromatography resin bead by virtue of its porous internal organization;

http://purl.obolibrary.org/obo/PATO_0000141

This quality concerns the organization of parts (spatial arrangement and connectivity) at whatever granularity is relevant (e.g., anatomical regions, microstructure, particle packing, macromolecular conformation).

PhysicalStructure(x) → MorphologicalQuality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

morphological quality that inheres in a material entity by virtue of the relative positions, arrangement, and connectivity of the material parts within that entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'physical structure' then x is a 'morphological quality' and is 'quality of' some 'material entity'

porosity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the porosity of a chromatography resin bed; the porosity of a filter membrane; the porosity of a lyophilized drug product cake; the porosity of a packed powder bed; the porosity of a porous ceramic support

https://www.sciencedirect.com/topics/engineering/porosity and https://www.iso.org/obp/ui#iso:std:iso:3252:ed-6:v1:en:term:3.3.48

Porosity(x) → VolumeFraction(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m) ∧ ∀s (hasMagnitudeBasisInBearerPart(x, s) → (Site(s) ∧ properContinuantPartOfAtSomeTime(s, m))))

true

volume fraction that is determined by the pore or void volume of a material entity relative to the total volume of that material entity

There are insufficient constructs to create a set of necessary and sufficient conditions

if x is a 'porosity' then x is a 'volume fraction' that is the 'quality of' some 'material entity', and if x 'has magnitude basis in bearer part' some s, then s is a 'site' that is a 'proper continuant part of at some time' that same 'material entity'

powder form https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the powder form of dried cell culture medium; the powder form of a powdered excipient lot; the powder form of spray-dried lactose; the powder form of a powdered buffer component

https://www.edqm.eu/documents/52006/389906/standard_terms_internal_vocabularies_for_pharmaceutical_dose_forms.pdf/dd395dc1-4d44-9c2e-ce7f-0d788d57b328?t=1651562025434& and https://emmo-repo.github.io/emmo.html

PowderForm(x) → ParticulateForm(x)

true

particulate form that inheres in a material entity by virtue of being physically organized as dry, finely divided, discrete solid particles

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'powder form' then x is a 'particulate form'

pressure https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the pressure of compressed air against the inner surface of a supply line; the pressure of gas in a bioreactor headspace; the pressure of liquid at the inlet of a chromatography column; the pressure of steam in an autoclave chamber

http://purl.obolibrary.org/obo/PATO_0001025

Pressure(x) → RelationalQuality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

relational quality of a material entity that is the amount of normal force exerted by that material entity per unit area across a surface, boundary, or interface

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'pressure' then x is a 'relational quality' that is the 'quality of' some 'material entity'

quality homogeneity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Quality homogeneity of pH throughout a prepared buffer lot after mixing; Quality homogeneity of osmolality throughout a cell culture medium lot before release for use; Quality homogeneity of electrical conductivity throughout a chromatography buffer preparation;

QualityHomogeneity(x) → Homogeneity(x) ∧ ∃m∃q (MaterialEntity(m) ∧ Quality(q) ∧ qualityOf(x, m) ∧ specificallyDependsOn(x, q) ∧ qualityOf(q, m))

true

homogeneity inhering in a material entity by virtue of the extent to which one or more qualities of that material entity are uniformly distributed throughout that material entity

There are insufficient constructs to create a set of necessary and sufficient conditions.

if x is a 'quality homogeneity', then x is a 'homogeneity' that is the 'quality of' some 'material entity' m, and x 'specifically depends on' some 'quality' q that is also the 'quality of' that same material entity m

radius https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Radius of a chromatography resin bead; Radius of a spherical protein aggregate particle; Radius of a filter pore; Radius of a tubing lumen in a single-use assembly; Radius of a circular chromatography column bed; Radius of a bioreactor vessel cross-section.

http://purl.obolibrary.org/obo/PATO_0002390

Radius(x) → Length(x)

true

length that is the straight-line spatial extent from the center of a circular or spherical bearer to one of its boundary points

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'radius' then x is a 'length'

ratio https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the mass fraction of glucose in a dry powder medium; the volume fraction of gas in a foam; the porosity of a chromatography resin bed; the viable cell fraction of a cell suspension;

http://purl.allotrope.org/ontologies/quality#AFQ_0000005

Ratio(x) → RelationalQuality(x)

true

relational quality that is determined by the magnitude of one quality relative to the magnitude of another quality of the same kind

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'ratio' then x is a 'relational quality'

semi-crystalline structure https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the semi-crystalline structure of polyethylene; the semi-crystalline structure of polypropylene; the semi-crystalline structure of a polymer film containing crystalline lamellae and amorphous regions; the semi-crystalline structure of a partially crystallized excipient;

SemiCrystallineStructure(x) → PhysicalStructure(x) ∧ ∃m∃s∃a∃c∃as∃cs(MaterialEntity(m) ∧ qualityOf(x,m) ∧ SolidAggregateState(s) ∧ hasQuality(m,s) ∧ MaterialEntity(a) ∧ MaterialEntity(c) ∧ a ≠ c ∧ properContinuantPartOfAtAllTimes(a,m) ∧ properContinuantPartOfAtAllTimes(c,m) ∧ AmorphousStructure(as) ∧ hasQuality(a,as) ∧ CrystallineStructure(cs) ∧ hasQuality(c,cs))

true

physical structure that inheres in a solid material entity by virtue of that entity having both crystalline regions and amorphous regions interspersed as structural parts

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'semi-crystalline structure' then x is a 'physical structure' that is the 'quality of' some 'material entity' that 'has quality' some 'solid aggregate state' and 'has proper continuant part at all times' two distinct 'material entities', one that 'has quality' some 'amorphous structure' and another that 'has quality' some 'crystalline structure'

solid aggregate state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the solid aggregate state of sodium chloride crystals; the solid aggregate state of powdered cell culture medium; the solid aggregate state of granular cell culture medium; the solid aggregate state of a lyophilized drug product;

http://purl.allotrope.org/ontologies/quality#AFQ_0000112

Solid aggregate state should be distinguished from particulate flow. A powder, granulated material, or bead population may flow as a bulk material because its discrete solid particles or particle aggregates can rearrange relative to one another during pouring, shaking, mixing, or transfer. This kind of particulate flow does not mean that the material entity bears a fluid aggregate state. Fluid-like flow, in this context, refers to continuous deformation of a material as a connected liquid, gas, or plasma, rather than motion produced by rearrangement of separate solid units.

SolidAggregateState(x) → AggregateState(x)

true

aggregate state of a material entity in which the constituent material parts are sufficiently constrained in their relative motion that the material entity has a definite volume and resists continuous, fluid-like flow

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'solid aggregate state' then x is an 'aggregate state'

specific surface area https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ powdered cell culture medium with high specific surface area; porous chromatography resin particles with high specific surface area; mesoporous silica with high specific surface area to support palladium to be used as catalyst in the hydrogenation of carbon dioxide; activated carbon with high available surface for adsorption;

https://goldbook.iupac.org/terms/view/S05806

SpecificSurfaceArea(x) → Quality(x) ∧ ∃m∃s (MaterialEntity(m) ∧ qualityOf(x, m) ∧ SolidAggregateState(s) ∧ hasQuality(m, s))

true

quality of a solid material entity that is its total surface area per unit mass

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'specific surface area' then x is a 'quality' that is the 'quality of' some 'material entity' that 'has quality' some 'solid aggregate state'

stability https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Stability of a drug substance batch during refrigerated storage; Stability of a formulated drug product during accelerated stability testing; Stability of a cell culture medium lot during storage at 2–8 °C; Stability of a buffer preparation during a defined hold interval;

https://database.ich.org/sites/default/files/Q1A%28R2%29%20Guideline.pdf and https://goldbook.iupac.org/terms/view/08027

Stability(x) → Capability(x) ∧ ∃m (MaterialEntity(m) ∧ capabilityOf(x, m))

true

capability of a material entity to resist change in one or more of its attributes during a particular process

There are insufficient constructs to create a set of necessary and sufficient conditions.

if x is a 'stability' then x is a 'capability' that is the 'capability of' some 'material entity'

sterile material state https://spec.industrialontologies.org/ontology/biopharma/BiopharmaManufacturingExecution/ the sterile material state of culture medium after filtration through a sterilizing-grade membrane filter; the sterile material state of a stainless-steel bioreactor vessel after steam sterilization; the sterile material state of glassware after autoclaving;

https://www.fda.gov/regulatory-information/search-fda-guidance-documents/content-and-format-premarket-notification-510k-submissions-liquid-chemical-sterilantshigh-level

sterile material state applies to a material entity when the relevant condition that remains unchanged is that the material entity is free of viable microorganisms. It may apply to process materials, vessels, equipment parts, containers, closures, filters, tubing assemblies, fluid pathways, or other product-contact materials expected to remain sterile. In regulated manufacturing contexts, sterile status is typically established through validated sterilization or aseptic processing controls and sterility assurance, rather than by direct demonstration of the absence of every viable microorganism. Sterile material state should be distinguished from clean state or disinfected state, which may involve reduction or removal of bioburden without necessarily rendering the material entity free of viable microorganisms.

SterileMaterialState(x) → MaterialState(x)

true

material state in which a participating material entity is free of viable microorganisms

There are insufficient constructs to represent absence of viable microorganisms

if x is a 'sterile material state' then x is a 'material state'

temperature https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the temperature of cell culture medium in a bioreactor; the temperature of a buffer during preparation; the temperature of a formulation during refrigerated storage;

http://purl.obolibrary.org/obo/PATO_0000146 and https://www.nist.gov/si-redefinition/kelvin/kelvin-thermodynamic-temperature and https://www.bipm.org/en/si-base-units/kelvin

1) The microscopic degrees of freedom relevant to temperature may include translational, rotational, vibrational, electronic, and collective modes, depending on the composition and physical state of the material entity. 2) Temperature is related to average thermal energy per microscopic degree of freedom but is not identical with total internal energy or with average translational kinetic energy. The precise relationship depends on which degrees of freedom are thermally accessible and may require qualification for quantum or non-equilibrium materials.

Temperature(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m))

true

quality of a material entity whose magnitude characterizes the average thermal energy per microscopic degree of freedom of that material entity

There are insufficient constructs to create necessary and sufficient conditions.

if x is a 'temperature' then x is a 'quality' that is the 'quality of' some 'material entity'

thermal stability https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Thermal stability of a drug substance batch during refrigerated storage; Thermal stability of a protein formulation during accelerated stability testing at elevated temperature; Thermal stability of a cell culture medium lot during storage at 2–8 °C; Thermal stability of a process intermediate during a defined room-temperature hold;

ThermalStability(x) → Stability(x)

true

stability that is the capability of a material entity to resist change in one or more of its attributes during exposure to a particular temperature condition

There are insufficient constructs to create a set of necessary and sufficient conditions.

if x is 'thermal stability' then x is a 'stability'

viscosity https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ cell culture medium has low viscosity at 37 °C; concentrated monoclonal antibody formulation has elevated viscosity at 20 °C to 25 °C; glycerol-containing cryopreservation medium has higher viscosity at low temperature; chromatography buffer has viscosity relevant to column pressure drop;

https://www.sciencedirect.com/topics/engineering/fluid-viscosity and https://pmc.ncbi.nlm.nih.gov/articles/PMC1258811/ and http://purl.obolibrary.org/obo/PATO_0000992

1) Viscosity is a material quality grounded in interactions among constituents of a fluid. In solutions and suspensions it reflects, among other factors, solvent–solute interactions, concentration, molecular association or aggregation, and the size and shape of dissolved or suspended entities. These features condition the degree of internal friction opposing relative motion within the fluid. 2) For a Newtonian fluid, viscosity is constant with respect to shear rate under specified conditions and characterizes the fluid's resistance to shear during agitation, pressure-driven flow, or gravity-driven flow. 3) For non-Newtonian fluids, such as blood, polymer solutions, gels, paints, or starch suspensions, apparent viscosity may vary with shear rate, shear stress, or the duration of applied shear. 4) In bioprocessing and formulation, viscosity affects mixing efficiency and mixing time, the shear environment experienced by cells or particles, pumpability and pressure drop, filtration behavior, and the maintenance of homogeneous distributions of solutes or suspended matter. 5) Process actions such as adjusting temperature or formulation composition may be used to manage viscosity so that transfer and mixing operations remain predictable and controlled.

Viscosity(x) → Quality(x) ∧ ∃m (MaterialEntity(m) ∧ qualityOf(x, m) ∧ ∃s (FluidAggregateState(s) ∧ hasQuality(m, s)))

true

quality of a fluid that is its resistance to shear deformation, manifested as internal friction opposing relative motion between adjacent parts of the fluid

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'viscosity' then x is a 'quality' that is the 'quality of' some 'material entity' that 'has quality' some 'fluid aggregate state'

volume https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ Volume of a buffer preparation in a mixing vessel; Volume of cell culture medium in a bioreactor; Volume of a process intermediate collected after filtration; Internal volume of a single-use bag; Working volume of a bioreactor vessel; Volume of a drug product fill in a vial.

http://purl.obolibrary.org/obo/PATO_0000918

Volume(x) → PhysicalSize(x)

true

physical size that is the three-dimensional spatial extent of a bearer

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'volume' then x is a 'physical size'

volume fraction https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the volume fraction of gas bubbles in a foam; the volume fraction of ethanol in an aqueous solution; the volume fraction of solids in a slurry; the volume fraction of oil droplets in an emulsion; the volume fraction of liquid phase in a two-phase material

http://purl.allotrope.org/ontologies/quality#AFQ_0000169

VolumeFraction(x) → Fraction(x)

true

fraction of a material entity that is determined by the volume of a specified material entity or site that is a continuant part of that material entity relative to the total volume of that material entity

There are insufficient constructs for creating a set of necessary and sufficient conditions

if x is a 'volume fraction' then x is a 'fraction'

has magnitude basis in bearer part https://spec.industrialontologies.org/ontology/biopharma/BiopharmaReferenceOntologyAttributes/ the humidity of a gas has magnitude basis in water molecules that are parts of the gas; the viable cell density of a cell culture material has magnitude basis in viable cells that are parts of the culture material; the aluminum fraction of a material has magnitude basis in elemental aluminum that is part of the material; the porosity of a solid material has magnitude basis in pore sites that are parts of the material

1) A bearer part provides a basis for the magnitude of a quality when the magnitude depends, at least in part, on the presence, amount, state, structure, arrangement, distribution, or other relevant characteristics of parts of that kind. These examples are illustrative rather than exhaustive. The relation does not imply that an individual related part or parts of the specified kind are the sole basis for the magnitude. 2) The relation is intended primarily for use in class axioms that constrain the kinds of bearer parts relevant to a quality type. Extensions of generic quality terms are expected to use the relation to identify the relevant bearer-part type. For example, 'glucose concentration' may be constrained as a 'concentration' that 'has magnitude basis in bearer part' only 'glucose molecule'. It is not required that the relation be asserted whenever an instance of the quality type is represented. 3) A universal restriction using 'only' specifies the type of material entity or site that may be related as the relevant bearer part, without requiring that any such part exists. This permits, for example, a glucose concentration with magnitude zero when the bearer contains no glucose molecules.

relation from a quality to a material entity or site that is a continuant part of the quality's bearer and provides a basis for the magnitude of that quality